title: CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.
abstract: BACKGROUND
  Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism.
  
  
  RESULTS
  We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms.
  
  
  BACKGROUND
  Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083, Turkey.
authors.forename: Gamze
authors.initials: G
authors.lastname: Abaka
authors.forename: Türker
authors.initials: T
authors.lastname: Bıyıkoğlu
authors.forename: Cesim
authors.initials: C
authors.lastname: Erten
mesh_terms: D000465:Algorithms; D060847:Metabolic Engineering; D053858:Metabolic Networks and Pathways